Vaccine-Associated Recombination and Virulence Heterogeneity of GI-19 (QX Type) Infectious Bronchitis Virus in Eastern and Southern China, 2024-2025.

Abstract

Infectious bronchitis (IB) virus (IBV) remains a major pathogen threatening the poultry industry. Its rapid mutation and recombination continuously generate variants that disseminate worldwide. Between May 2024 and February 2025, 49 field strains were isolated from chickens vaccinated with live-attenuated IBV vaccines (H120, 4/91, or QXL87) in four Chinese provinces (Jiangsu, Anhui, Shandong, and Guangdong). Based on full-length S1 gene sequencing, all isolates were classified into genotype GI, including lineages GI-13 and GI-19. Phylogenetic analysis revealed that GI-19 (QX-type) comprised as much as 83.67%, with the nucleotide homology of the S1 gene to QXL87 varying from 93.4% to 99.8%. Recombination analysis indicated that the S1 genes of three isolates incorporate QXL87 and 4/91 genetic material, possibly arising from recombination between the QX-type and 4/91 vaccine strains. Virulence assessment in 1-day-old specific-pathogen-free (SPF) chickens demonstrated that four phylogenetically distant QX-type strains and one recombinant strain (with QXL87 as the major parent) induced varying degrees of tissue damage and mortality. Cross-neutralization assays demonstrated reduced antigenic relatedness between the circulating isolates and QXL87 vaccine strain. Structural mapping analysis further indicated that three amino acid mutations within the N-terminal domain (NTD) and two amino acid mutations in the C-terminal domain (CTD) of the S1 subunit alter its overall conformation, potentially leading to antigenic variation and facilitating immune evasion. Overall, these findings offer timely insights into the epidemiology and virulence heterogeneity of QX-IBV, providing valuable references for optimizing vaccine selection and development, as well as for preventing and controlling the disease.